The Forkhead transcription factor Hcm1 regulates chromosome
segregation genes and fills the S-phase gap in the transcriptional
circuitry of the cell cycle

Abstract

Transcription patterns shift dramatically as cells transit from one
phase of the cell cycle to another. To better define this
transcriptional circuitry, we collected new microarray data across the
cell cycle of budding yeast. The combined analysis of these data with
three other cell cycle data sets identifies hundreds of new highly
periodic transcripts and provides a weighted average peak time for
each transcript. Using these data and phylogenetic comparisons of
promoter sequences, we have identified a late S-phase-specific
promoter element. This element is the binding site for the forkhead
protein Hcm1, which is required for its cell cycle-specific
activity. Among the cell cycle-regulated genes that contain conserved
Hcm1-binding sites, there is a significant enrichment of genes
involved in chromosome segregation, spindle dynamics, and
budding. This may explain why Hcm1 mutants show 10-fold elevated rates
of chromosome loss and require the spindle checkpoint for
viability. Hcm1 also induces the M-phase-specific transcription
factors FKH1, FKH2, and NDD1, and two cell cycle-specific
transcriptional repressors, WHI5 and YHP1. As such, Hcm1 fills a
significant gap in our understanding of the transcriptional circuitry
that underlies the cell cycle.